There are no special tricks or difficulty getting the bot to work with Isboxer - at least not when you try to run no more than 3 instances. People have had trouble before running more than 3 instances on one computer with the bot not being able to recognize the windows correctly. I usually did 2 instances for flash points since the companions did such a great job anyway, so never really had any issues. Hard mode used to be more tricky and needed a different setup running on 2 different computers. Not sure how it would be in the new system. Will see...
Let us know if you have specific issues and maybe someone can help or advice?